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H3N2 aptamer
Description
In 2006, Gopinath SCB, Misono TS, Kawasaki K, et al. used the SELEX method to select the aptamer binds specifically to the haemagglutinin (HA) region of the target strain A/Panama/2007/1999(H3N2) and failed to recognize other human influenza viruses, including another strain with the same subtype, H3N2. This study demonstrates the potential application of aptamers in influenza virus genotyping and functional research, and may be helpful for developing new antiviral strategies[1].SELEX
In 2006, Gopinath SCB, Misono TS, Kawasaki K, et al. obtained aptamers from a random RNA sequence library through the SELEX method. Among the RNA molecules obtained from the tenth round of screening, 17 clones were cloned and sequenced, and their sequences were classified into three main groups. They aslo used surface plasmon resonance (SPR) to identify the phosphate groups in the ligand that are crucial for HA binding, and mapped the smallest RNA motif that can bind to A/Panama virus HA[1].
Detailed information are accessible on SELEX page.
Structure
The 2D structure of the figure is based on the article by ribodraw tool to draw. P30-10-16 apatamer binds to haemagglutinin (HA) region of the target strain A/Panama/2007/1999(H3N2)[1].5'-GGGAGAAUUCCGACCAGAAGGGUUAGCAGUCGGCAUGCGGUACAGACAGACCUUUCCUCUCUCCUUCCUCUUCU-3'
Ligand information
SELEX ligand
Binds to sialic acid-containing receptors on the cell surface, bringing about the attachment of the virus particle to the cell. This attachment induces virion internalization either through clathrin-dependent endocytosis or through clathrin- and caveolin-independent pathway. Plays a major role in the determination of host range restriction and virulence. Class I viral fusion protein. Responsible for penetration of the virus into the cell cytoplasm by mediating the fusion of the membrane of the endocytosed virus particle with the endosomal membrane. Low pH in endosomes induces an irreversible conformational change in HA2, releasing the fusion hydrophobic peptide. Several trimers are required to form a competent fusion pore.-----From Uniprot
| Name | Uniprot ID | Pfam | MW | Amino acids sequences | PDB | Gene ID |
|---|---|---|---|---|---|---|
| Haemagglutinin (HA) region of H3N2 | A0A097PF13 | IPR000149 | 63.635 kDa | MKTIIALSYILCLVFAQKLPGNDNSTATLCLGHHAVSNGTLVKTITNDQIEVTNATELVQSSSTGRICDSPHQILDGENCTLIDALLGDPHCDGFQNKEWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEFNNESFNWTGVAQNGTSSACKRRSNKSFFSRLNWLHQLNYKYPALNVTMPNNEKFDKLYIWGVLHPSTDSDQISLYAQASGRVTVSTKRSQQTVIPNIGSRPWVRGVSSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRITYGACPRYVKQNTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGTGQAADLKSTQAAINQINGKLNRLIEKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFERTKKQLRENAEDMGNGCFKIYHKCDNACIGSIRNGTYDHDVYRDEALNNRFQIKGVELKSGYKDWILWISFAISCFLLCVVLLGFIMWACQKGNIRCNICI | NA | AY832929.1 |
Some isolated sequences bind to the affinity of the protein.
| Name | Sequence | Ligand | Affinity |
|---|---|---|---|
| P30-10-16 | 5'-GGGAGAAUUCCGACCAGAAGGGUUAAGCAGUCGGCAUGCGGUACAGACAGACCUUUCCUCUCUCCUUCCUCUUCU-3' | Haemagglutinin (HA) region of H3N2 | 188 pM |
References
[1] An RNA aptamer that distinguishes between closely related human influenza viruses and inhibits haemagglutinin-mediated membrane fusion.Gopinath, S. C. B., Misono, T. S., Kawasaki, K., Mizuno, T., Imai, M., Odagiri, T., & Kumar, P. K. R.
The Journal of general virology, 87(Pt 3), 479–487. (2006)